SMTL ID : 5csy.1

Disproportionating enzyme 1 from Arabidopsis - acarbose soak

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

1 x BGC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-GLC.1: 15 residues within 4Å: Chain A: D.317, L.318, F.319, Q.324, D.361, H.362, E.408, L.410, G.411, F.434, N.442, H.444, D.461 Ligands: BGC-GLC-GLC-GLC.2, BGC-GLC-GLC-GLC.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.411, A:N.442, A:Q.324, A:D.361, A:H.362, A:H.362, A:E.408, A:D.461, A:D.461 Salt bridges: A:H.444 Water bridges: A:R.359, A:L.410

1 x BGC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-GLC-GLC.2: 17 residues within 4Å: Chain A: D.118, S.122, Y.124, A.125, L.325, W.326, R.359, D.361, H.460, D.461, N.525, P.527, A.528, T.529, E.530, W.534 Ligands: BGC-GLC-GLC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.359, A:H.460, A:D.461, A:N.525, A:L.325 Water bridges: A:Y.124, A:D.461

1 x GLC- GLC- AC1- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-AC1-GLC-GLC-GLC.3: 26 residues within 4Å: Chain B: D.118, S.122, Y.124, A.125, D.317, L.318, F.319, Q.324, L.325, W.326, G.327, R.359, D.361, H.362, E.408, L.410, G.411, F.434, H.444, H.460, D.461, N.525, P.527, A.528, T.529, E.530 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:L.325, B:Q.324, B:R.359, B:R.359, B:H.362, B:H.362, B:E.408, B:E.408, B:L.410 Hydrophobic interactions: B:W.326, B:P.527 Water bridges: B:Y.124, B:I.284, B:E.408, B:E.408, B:L.410

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: T.176, F.249, L.252, F.253, K.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.256 EDO.5: 6 residues within 4Å: Chain A: A.129, N.130, M.282, R.347, R.350, Y.355 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.347, A:R.347, A:Y.355, A:Y.355 EDO.6: 2 residues within 4Å: Chain A: P.230, A.238 No protein-ligand interaction detected (PLIP) EDO.7: 8 residues within 4Å: Chain A: A.351, Q.352, Y.355, D.356, E.357, C.358, I.403, K.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.351, A:K.404 EDO.8: 7 residues within 4Å: Chain A: L.75, L.76, H.460, Q.513, M.524, W.536 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.75, A:Q.513 Water bridges: A:H.77 EDO.9: 11 residues within 4Å: Chain A: T.459, H.460, N.462, D.463, T.464, P.511, Q.513, D.514, R.523, M.524 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.460, A:D.514, A:M.524 Water bridges: A:I.465 EDO.10: 5 residues within 4Å: Chain B: T.176, F.249, L.252, F.253, K.256 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.256 EDO.11: 8 residues within 4Å: Chain B: A.351, Q.352, Y.355, D.356, E.357, C.358, I.403, K.404 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.351, B:K.404 EDO.12: 7 residues within 4Å: Chain B: L.75, L.76, L.112, H.460, M.512, Q.513, M.524 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.512, B:Q.513, B:Q.513 Water bridges: B:H.77 EDO.13: 10 residues within 4Å: Chain B: T.459, H.460, N.462, D.463, T.464, P.511, Q.513, D.514, R.523, M.524 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.514, B:M.524 EDO.14: 6 residues within 4Å: Chain B: S.521, R.523, N.525, T.526, G.532, N.533 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.521, B:T.526, B:T.526, B:N.533

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Neill, E.C. et al., Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1). J.Biol.Chem. (2015)

Release Date

2015-11-04

Peptides

4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic

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